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- PDB-3imk: Crystal structure of Putative molybdenum carrier protein (YP_4618... -

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Basic information

Entry
Database: PDB / ID: 3imk
TitleCrystal structure of Putative molybdenum carrier protein (YP_461806.1) from SYNTROPHUS ACIDITROPHICUS SB at 1.45 A resolution
ComponentsPutative molybdenum carrier protein
KeywordsMETAL BINDING PROTEIN / YP_461806.1 / Putative molybdenum carrier protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homologyCircularly permutated YpsA SLOG / Circularly permutated YpsA SLOG family / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-PG6 / Hypothetical cytosolic protein
Function and homology information
Biological speciesSyntrophus aciditrophicus SB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative molybdenum carrier protein (YP_461806.1) from SYNTROPHUS ACIDITROPHICUS SB at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative molybdenum carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3036
Polymers17,4631
Non-polymers8405
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.250, 59.255, 64.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative molybdenum carrier protein


Mass: 17463.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophus aciditrophicus SB (bacteria)
Gene: SYNAS_17590, SYN_02013, YP_461806.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q2LU76

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Non-polymers , 5 types, 208 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10.0000% Glycerol, 5.0000% PEG-1000, 30.0000% PEG-600, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.979221
ReflectionResolution: 1.45→28.479 Å / Num. obs: 28613 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.264 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.45-1.50.5932.3159704895193.3
1.5-1.560.4063.3180895366198.1
1.56-1.630.3134.3181955400199.1
1.63-1.720.235.8192425686198.9
1.72-1.830.158.4185075449199.2
1.83-1.970.09612.5182195363199.2
1.97-2.170.05818.9184305425199.2
2.17-2.480.0424.7181565333199.2
2.48-3.120.03231.4184665382199.1
3.12-28.4790.02739.7184305419198.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→28.479 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.835 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROL (GOL), 2-(N-MORPHOLINO)-ETHANESULFONIC ACID (MES) AND PEG1000 OR PEG600 FRAGMENT(PG4 AND PG6) MOLECULES ARE MODELED BASED ON CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1450 5.1 %RANDOM
Rwork0.152 ---
obs0.154 28572 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.09 Å2 / Biso mean: 17.087 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1208 0 55 203 1466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211351
X-RAY DIFFRACTIONr_bond_other_d0.0010.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9981816
X-RAY DIFFRACTIONr_angle_other_deg0.94232293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2145166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39524.54555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98715215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.099156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
X-RAY DIFFRACTIONr_nbd_refined0.2270.2272
X-RAY DIFFRACTIONr_nbd_other0.190.2937
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2654
X-RAY DIFFRACTIONr_nbtor_other0.0880.2605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.223
X-RAY DIFFRACTIONr_mcbond_it1.6493886
X-RAY DIFFRACTIONr_mcbond_other0.3883332
X-RAY DIFFRACTIONr_mcangle_it2.16151311
X-RAY DIFFRACTIONr_scbond_it3.8688583
X-RAY DIFFRACTIONr_scangle_it5.21111505
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 110 -
Rwork0.237 1854 -
all-1964 -
obs--93.66 %
Refinement TLS params.Method: refined / Origin x: 24.4983 Å / Origin y: 2.9987 Å / Origin z: -7.8432 Å
111213212223313233
T-0.0393 Å2-0.0084 Å2-0.0029 Å2--0.0261 Å2-0.0017 Å2---0.0335 Å2
L0.6397 °2-0.2603 °2-0.1236 °2-1.0363 °20.379 °2--0.8597 °2
S-0.0158 Å °0.013 Å °0.0159 Å °-0.007 Å °0.056 Å °-0.0114 Å °0.0504 Å °-0.0258 Å °-0.0402 Å °

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